Contacts of the helix formed by residues 23 - 32 (chain L) in PDB entry 4IBL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 23 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L CYS* 1.3 76.2 - - - +
24L PHE* 1.3 67.4 + - - +
25L CGU 3.5 6.0 + - - +
26L CGU 3.0 32.9 + - - +
27L ALA* 3.0 19.8 + - - +
41L TRP* 3.6 5.2 - - - -
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Residues in contact with PHE 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L SER* 1.3 73.4 - - - +
25L CGU 1.3 66.7 + - + +
27L ALA* 3.3 3.3 + - - +
28L ARG* 2.8 43.4 + - + +
34L ALA* 5.7 2.0 - - - -
37L THR* 3.4 30.3 - - + -
38L LYS* 4.8 6.5 - - + -
41L TRP* 3.3 57.0 - + + +
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Residues in contact with CGU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L SER* 3.3 6.0 + - - +
24L PHE* 1.3 84.3 + - + +
26L CGU 1.3 62.8 + - - +
28L ARG* 2.9 37.4 + - - +
29L CGU 2.9 43.5 + - + +
203L MG 2.0 48.2 - - - -
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Residues in contact with CGU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L CGU 5.0 2.3 - - - -
16L CGU 2.9 12.0 - - + -
21L GLN 4.0 0.7 - - - -
22L CYS* 3.2 14.7 - - + -
23L SER* 3.0 39.7 + - - +
25L CGU 1.3 76.3 + - - +
27L ALA* 1.4 65.2 + - - +
29L CGU 3.3 8.5 + - - +
30L ILE* 3.3 27.0 + - + +
204L CA 3.0 21.4 - - - -
205L RB 3.1 12.3 - - - -
206L MG 2.0 54.4 - - - -
211L RB 2.9 21.0 - - - -
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Residues in contact with ALA 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L CYS* 4.3 2.5 - - - -
22L CYS* 4.1 8.0 - - - -
23L SER 3.0 10.0 + - - +
24L PHE 3.6 7.2 - - - +
26L CGU 1.4 79.3 + - - +
28L ARG* 1.3 57.7 + - - +
30L ILE* 3.0 13.4 + - - +
31L PHE* 2.9 37.9 + - + -
37L THR* 4.3 3.8 - - + -
40L PHE* 3.8 34.1 - - + -
41L TRP* 4.4 6.7 - - + -
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Residues in contact with ARG 28 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24L PHE* 2.8 31.2 + - + +
25L CGU 2.9 30.7 + - - +
27L ALA* 1.3 72.5 - - - +
29L CGU 1.3 91.1 + - - +
32L LYS* 2.6 63.4 + - - +
33L ASP 5.2 0.7 - - - +
34L ALA* 5.6 3.6 - - - +
37L THR* 3.5 28.6 - - + +
203L MG 3.7 0.4 - - - -
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Residues in contact with CGU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L CGU 2.9 31.2 + - + +
26L CGU 3.4 9.6 - - - +
27L ALA 3.2 0.4 - - - -
28L ARG* 1.3 95.8 + - - +
30L ILE* 1.3 62.2 + - + +
32L LYS* 3.7 21.0 - - - +
203L MG 2.0 49.7 - - - -
204L CA 2.7 16.5 - - - -
205L RB 2.5 31.7 - - - -
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Residues in contact with ILE 30 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11L GLY* 4.6 6.7 - - - -
12L SER* 4.0 10.5 - - - +
13L LEU* 3.9 38.4 - - + +
16L CGU 3.8 26.7 - - + -
17L CYS* 4.2 14.8 - - - -
26L CGU 3.3 20.3 + - - +
27L ALA* 3.0 8.1 + - - +
29L CGU 1.3 80.3 + - + +
31L PHE* 1.3 75.6 + - + +
32L LYS* 4.1 10.7 + - - +
160T SER* 5.9 2.9 - - - -
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Residues in contact with PHE 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L LEU* 3.9 28.0 - - + -
27L ALA* 2.9 28.0 + - + -
30L ILE* 1.3 82.6 - - + +
32L LYS* 1.3 58.8 + - - +
33L ASP* 2.8 16.3 + - - +
36L ARG* 3.9 19.7 + - + -
37L THR* 3.4 33.2 - - - +
40L PHE* 3.5 46.0 - + + -
158T TRP* 4.1 28.3 - + - -
160T SER 5.3 1.9 - - - +
186T CYS* 3.9 24.5 - - - -
207T VAL* 4.6 2.0 - - + -
209T CYS* 4.0 3.6 - - - -
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Residues in contact with LYS 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L ARG* 2.6 48.4 + - - +
29L CGU 3.7 23.8 - - - +
30L ILE 4.2 8.2 + - - +
31L PHE* 1.3 73.0 - - - +
33L ASP* 1.3 61.5 + - - +
34L ALA* 3.5 1.9 + - - -
37L THR* 3.9 1.3 + - - -
160T SER 5.4 7.8 + - - +
161T SER* 6.2 1.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il